Embryo formation requires tight regulation and coordination of adhesion in multiple cell types. By undertaking imaging, three-dimensional (3D) reconstructions and genetic analysis during posterior midgut morphogenesis in Drosophila, we find a new requirement for the conserved fibroblast growth factor (FGF) signaling pathway in the maintenance of epithelial cell adhesion through FGF modulation of zygotic E-cadherin. During Drosophila gastrulation, primordial germ cells (PGCs) are transported with the posterior midgut while it undergoes dynamic cell shape changes. In embryos mutant for the FGF signaling pathway components Branchless and Breathless, zygotic E-cadherin is not targeted to adherens junctions, causing midgut pocket collapse, which impacts on PGC movement. We find that the ventral midline also requires FGF signaling to maintain cell-cell adhesion. We show that FGF signaling regulates the distribution of zygotic E-cadherin during early embryonic development to maintain cell-cell adhesion in the posterior midgut and the ventral midline, a role that is likely crucial in other tissues undergoing active cell shape changes with higher adhesive needs.